AUTHOR=Sabat Artur J. , Durfee Tim , Baldwin Schuyler , Akkerboom Viktoria , Voss Andreas , Friedrich Alexander W. , Bathoorn Erik 

TITLE=The complete genome sequence of unculturable Mycoplasma faucium obtained through clinical metagenomic next-generation sequencing

JOURNAL=Frontiers in Cellular and Infection Microbiology

VOLUME=14

YEAR=2024

URL=https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2024.1368923

DOI=10.3389/fcimb.2024.1368923

ISSN=2235-2988

ABSTRACT=<sec><title>Introduction</title><p>Diagnosing <italic>Mycoplasma faucium</italic> poses challenges, and it's unclear if its rare isolation is due to infrequent occurrence or its fastidious nutritional requirements.</p></sec><sec><title>Methods</title><p>This study analyzes the complete genome sequence of <italic>M. faucium</italic>, obtained directly from the pus of a sternum infection in a lung transplant patient using metagenomic sequencing.</p></sec><sec><title>Results</title><p>Genome analysis revealed limited therapeutic options for the <italic>M. faucium</italic> infection, primarily susceptibility to tetracyclines. Three classes of mobile genetic elements were identified: two new insertion sequences, a new prophage (phiUMCG-1), and a species-specific variant of a mycoplasma integrative and conjugative element (MICE). Additionally, a Type I Restriction-Modification system was identified, featuring 5’-terminally truncated <italic>hsdS</italic> pseudogenes with overlapping repeats, indicating the potential for forming alternative <italic>hsdS</italic> variants through recombination.</p></sec><sec><title>Conclusion</title><p>This study represents the first-ever acquisition of a complete circularized bacterial genome directly from a patient sample obtained from invasive infection of a primary sterile site using culture-independent, PCR-free clinical metagenomics.</p></sec>